Title: The Genie++ Hierarchical Clustering Algorithm with Noise Points
Detection
Description: A retake on the Genie algorithm - a robust
hierarchical clustering method
(Gagolewski, Bartoszuk, Cena, 2016 <DOI:10.1016/j.ins.2016.05.003>).
Now faster and more memory efficient; determining the whole hierarchy
for datasets of 10M points in low dimensional Euclidean spaces or
100K points in high-dimensional ones takes only 1-2 minutes.
Allows clustering with respect to mutual reachability distances
so that it can act as a noise point detector or a robustified version of
'HDBSCAN*' (that is able to detect a predefined number of
clusters and hence it does not dependent on the somewhat
fragile 'eps' parameter).
The package also features an implementation of economic inequity indices
(the Gini, Bonferroni index) and external cluster validity measures
(partition similarity scores; e.g., the adjusted Rand, Fowlkes-Mallows,
adjusted mutual information, pair sets index).
See also the 'Python' version of 'genieclust' available on 'PyPI', which
supports sparse data, more metrics, and even larger datasets.
Author: Marek Gagolewski [aut, cre, cph]
(<https://orcid.org/0000-0003-0637-6028>),
Maciej Bartoszuk [ctb],
Anna Cena [ctb],
Peter M. Larsen [ctb]
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between genieclust versions 0.9.3 dated 2020-07-30 and 0.9.4 dated 2020-07-31
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS | 5 +++++ src/c_compare_partitions.h | 12 ++++++------ src/c_genie.h | 12 ++++++------ src/c_matrix.h | 2 +- src/r_compare_partitions.cpp | 8 ++++---- 7 files changed, 33 insertions(+), 28 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis, especially raster data. Methods allow for low-level data manipulation as well as high-level global, local, zonal, and focal computation. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/terra/> to get started. The package is similar to the 'raster' package; but 'terra' is simpler and faster.
Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>),
Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>),
Karl Forner [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>)
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 0.8-5 dated 2020-07-28 and 0.8-6 dated 2020-07-31
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/scatter.Rd | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Interface to 'Matba Rofex' Trading API
Description: Execute API calls to the 'Matba Rofex' <https://apihub.primary.com.ar> trading platform. Functionality includes accessing account data and current holdings, retrieving investment quotes, placing and canceling orders, and getting reference data for instruments.
Author: Augusto Hassel [aut, cre],
Juan Francisco Gomez [ctb],
Matba Rofex [cph]
Maintainer: Augusto Hassel <mpi-augusto@primary.com.ar>
Diff between rRofex versions 2.0.2 dated 2020-07-14 and 2.0.3 dated 2020-07-31
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- build/rRofex.pdf |binary man/rRofex-package.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.5.4.1 dated 2020-07-01 and 0.5.4.3 dated 2020-07-31
DESCRIPTION | 8 MD5 | 36 +- R/Causal_matrix.R | 3 R/Causation.R | 37 -- R/Co_PM_dep.R | 20 - R/Dependence.R | 34 +- R/Dependence_base.R | 25 + R/Multivariate_Regression.R | 3 R/NNS_meboot.R | 2 R/Partial_Moments.R | 8 R/Regression.R | 262 +++++++++---------- R/dy_d_wrt.R | 91 +++--- R/gvload.R | 2 inst/doc/NNSvignette_Classification.html | 24 + inst/doc/NNSvignette_Clustering_and_Regression.html | 84 +++--- inst/doc/NNSvignette_Correlation_and_Dependence.html | 36 +- inst/doc/NNSvignette_Forecasting.html | 16 - man/Co.UPM.Rd | 2 man/NNS.meboot.Rd | 2 19 files changed, 343 insertions(+), 352 deletions(-)
Title: Algorithm to Compute Monitor Independent Movement Summary Unit
(MIMS-Unit)
Description: The MIMS-unit algorithm is developed to compute Monitor Independent
Movement Summary Unit, a measurement to summarize raw accelerometer data
while ensuring harmonized results across different devices. It also includes
scripts to reproduce results in the related publication
(John, D., Tang. Q., Albinali, F. and Intille, S. (2019) <doi:10.1123/jmpb.2018-0068>).
Author: Qu Tang [aut, cre] (<https://orcid.org/0000-0001-5415-0205>),
Dinesh John [aut],
Stephen Intille [aut],
mHealth Research Group [cph] (https://mhealthgroup.org)
Maintainer: Qu Tang <tang.q@northeastern.edu>
Diff between MIMSunit versions 0.9.1 dated 2020-05-20 and 0.9.2 dated 2020-07-31
DESCRIPTION | 12 MD5 | 70 NEWS.md | 12 R/aggregate_over_epoch.R | 44 R/combine_axes.R | 4 R/data.R | 2 R/extrapolate.R | 38 R/filter.R | 117 R/import_data.R | 2 R/interpolate.R | 8 R/mims_unit.R | 380 +- R/plotting.R | 4 R/simulate_data.R | 4 README.md | 2 data/sample_raw_accel_data.rda |binary inst/extdata/mhealth.csv | 4520 ------------------------------- inst/extdata/mhealth1.csv | 5480 +++----------------------------------- man/aggregate_for_mims.Rd | 22 man/aggregate_for_orientation.Rd | 22 man/bandlimited_interp.Rd | 4 man/bessel.Rd | 4 man/custom_mims_unit.Rd | 6 man/cut_off_signal.Rd | 2 man/extrapolate.Rd | 186 - man/generate_interactive_plot.Rd | 2 man/iir.Rd | 10 man/illustrate_signal.Rd | 2 man/import_mhealth_csv_chunked.Rd | 2 man/interpolate_signal.Rd | 8 man/mims_unit.Rd | 277 - man/remove_average.Rd | 4 man/sample_raw_accel_data.Rd | 2 man/sensor_orientations.Rd | 4 man/simulate_new_data.Rd | 2 man/sum_up.Rd | 2 man/vector_magnitude.Rd | 2 36 files changed, 1145 insertions(+), 10117 deletions(-)
Title: Cross-Platform File System Operations Based on 'libuv'
Description: A cross-platform interface to file system operations, built on
top of the 'libuv' C library.
Author: Jim Hester [aut, cre],
Hadley Wickham [aut],
libuv project contributors [cph] (libuv library),
Joyent, Inc. and other Node contributors [cph] (libuv library),
RStudio [cph, fnd]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between fs versions 1.4.2 dated 2020-06-30 and 1.5.0 dated 2020-07-31
fs-1.4.2/fs/src/libuv |only fs-1.5.0/fs/DESCRIPTION | 8 fs-1.5.0/fs/MD5 | 335 ++++++++++++------------- fs-1.5.0/fs/NAMESPACE | 3 fs-1.5.0/fs/NEWS.md | 18 + fs-1.5.0/fs/R/file.R | 4 fs-1.5.0/fs/R/fs_bytes.R | 42 +++ fs-1.5.0/fs/R/fs_path.R | 34 ++ fs-1.5.0/fs/R/fs_perms.R | 56 ++++ fs-1.5.0/fs/R/zzz.R | 30 ++ fs-1.5.0/fs/README.md | 78 ++--- fs-1.5.0/fs/inst/WORDLIST | 3 fs-1.5.0/fs/inst/doc/function-comparisons.html | 16 + fs-1.5.0/fs/src/Makevars | 18 - fs-1.5.0/fs/src/Makevars.win | 14 - fs-1.5.0/fs/src/dir.cc | 8 fs-1.5.0/fs/src/id.cc | 2 fs-1.5.0/fs/src/libuv-1.38.1 |only fs-1.5.0/fs/src/windows/getmode.cc | 8 fs-1.5.0/fs/tests/testthat/test-create.R | 11 fs-1.5.0/fs/tests/testthat/test-file.R | 4 fs-1.5.0/fs/tests/testthat/test-fs_bytes.R | 55 ++++ fs-1.5.0/fs/tests/testthat/test-fs_path.R | 33 ++ fs-1.5.0/fs/tests/testthat/test-fs_perms.R | 84 ++++++ fs-1.5.0/fs/tests/testthat/test-is.R | 15 - 25 files changed, 639 insertions(+), 240 deletions(-)
Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources,
including Global Biodiversity Information Facility ('GBIF'), 'USGSs'
Biodiversity Information Serving Our Nation ('BISON'), 'iNaturalist',
Berkeley 'Ecoinformatics' Engine, 'eBird', Integrated Digitized
'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information
System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes
functionality for retrieving species occurrence data, and combining
those data.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Karthik Ram [ctb],
Ted Hart [ctb],
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between spocc versions 1.0.8 dated 2020-02-11 and 1.1.0 dated 2020-07-31
spocc-1.0.8/spocc/man/fixnames-deprecated.Rd |only spocc-1.1.0/spocc/DESCRIPTION | 26 spocc-1.1.0/spocc/MD5 | 68 - spocc-1.1.0/spocc/NEWS.md | 22 spocc-1.1.0/spocc/R/fixnames.r | 86 - spocc-1.1.0/spocc/R/handle_sf.R |only spocc-1.1.0/spocc/R/handle_sp.R | 4 spocc-1.1.0/spocc/R/occ.r | 256 --- spocc-1.1.0/spocc/R/occ_funs.R |only spocc-1.1.0/spocc/R/plugins.r | 4 spocc-1.1.0/spocc/R/spocc-package.R | 1 spocc-1.1.0/spocc/README.md | 161 -- spocc-1.1.0/spocc/build/vignette.rds |binary spocc-1.1.0/spocc/inst/doc/spocc.Rmd | 337 +---- spocc-1.1.0/spocc/inst/doc/spocc.html | 868 ++++++------- spocc-1.1.0/spocc/man/figures |only spocc-1.1.0/spocc/man/fixnames-defunct.Rd |only spocc-1.1.0/spocc/man/occ.Rd | 53 spocc-1.1.0/spocc/man/occ_names.Rd | 6 spocc-1.1.0/spocc/man/spocc-package.Rd | 1 spocc-1.1.0/spocc/tests/fixtures/as_ala.yml |only spocc-1.1.0/spocc/tests/fixtures/as_ala_prep.yml |only spocc-1.1.0/spocc/tests/fixtures/as_bison.yml |only spocc-1.1.0/spocc/tests/fixtures/as_bison_prep.yml |only spocc-1.1.0/spocc/tests/fixtures/as_ecoengine.yml |only spocc-1.1.0/spocc/tests/fixtures/as_ecoengine_prep.yml |only spocc-1.1.0/spocc/tests/fixtures/as_gbif.yml |only spocc-1.1.0/spocc/tests/fixtures/as_gbif_prep.yml |only spocc-1.1.0/spocc/tests/fixtures/as_idigbio.yml |only spocc-1.1.0/spocc/tests/fixtures/as_idigbio_prep.yml |only spocc-1.1.0/spocc/tests/fixtures/as_inat.yml |only spocc-1.1.0/spocc/tests/fixtures/as_inat_prep.yml |only spocc-1.1.0/spocc/tests/fixtures/as_obis.yml |only spocc-1.1.0/spocc/tests/fixtures/as_obis_prep.yml |only spocc-1.1.0/spocc/tests/fixtures/as_vertnet.yml |only spocc-1.1.0/spocc/tests/fixtures/as_vertnet_prep.yml |only spocc-1.1.0/spocc/tests/fixtures/occ_vertnet.yml | 253 +-- spocc-1.1.0/spocc/tests/fixtures/print_methods.yml |only spocc-1.1.0/spocc/tests/testthat/test-as.ala.R |only spocc-1.1.0/spocc/tests/testthat/test-as.bison.R |only spocc-1.1.0/spocc/tests/testthat/test-as.ecoengine.R |only spocc-1.1.0/spocc/tests/testthat/test-as.gbif.R |only spocc-1.1.0/spocc/tests/testthat/test-as.idigbio.R |only spocc-1.1.0/spocc/tests/testthat/test-as.inat.R |only spocc-1.1.0/spocc/tests/testthat/test-as.obis.R |only spocc-1.1.0/spocc/tests/testthat/test-as.vertnet.R |only spocc-1.1.0/spocc/tests/testthat/test-occ.R | 20 spocc-1.1.0/spocc/tests/testthat/test-print_methods.R |only spocc-1.1.0/spocc/tests/testthat/test-taxize-integration.R | 6 spocc-1.1.0/spocc/vignettes/spocc.Rmd | 337 +---- spocc-1.1.0/spocc/vignettes/spocc.Rmd.og |only 51 files changed, 1067 insertions(+), 1442 deletions(-)
Title: Extraction of Medication Information from Clinical Text
Description: Function and support for medication and dosing information extraction from free-text clinical notes. Medication entities that can be extracted include drug name, strength, dose amount, dose, frequency, intake time, and time of last dose.
Author: Hannah Weeks [aut, cre],
Cole Beck [aut] (<https://orcid.org/0000-0002-6849-6255>),
Leena Choi [aut]
Maintainer: Hannah Weeks <hannah.l.weeks@vanderbilt.edu>
Diff between medExtractR versions 0.1 dated 2019-07-01 and 0.2 dated 2020-07-31
DESCRIPTION | 8 +- MD5 | 40 ++++++------- NEWS.md |only R/dosechange_vals.R | 2 R/extract_entities.R | 143 ++++++++++++++++++++++++++++++++--------------- R/extract_generic.R | 2 R/extract_lastdose.R | 2 R/medExtractR.R | 77 +++++++++++++++---------- R/rxnorm_druglist.R | 2 README.md |only data/dosechange_vals.rda |binary data/freq_vals.rda |binary data/intaketime_vals.rda |binary data/rxnorm_druglist.rda |binary data/time_regex.rda |binary man/dosechange_vals.Rd | 4 - man/extract_entities.Rd | 16 +++-- man/freq_vals.Rd | 6 + man/intaketime_vals.Rd | 6 + man/medExtractR.Rd | 21 +++++- man/rxnorm_druglist.Rd | 4 - man/time_regex.Rd | 6 + 22 files changed, 219 insertions(+), 120 deletions(-)
Title: Bayesian Inference for Causal Networks
Description: A Bayesian hybrid approach for inferring Directed Acyclic Graphs
(DAGs) for continuous, discrete, and mixed data. The algorithm can use the
graph inferred by another more efficient graph inference method as input;
the input graph may contain false edges or undirected edges but can help
reduce the search space to a more manageable size. A Bayesian Markov chain
Monte Carlo algorithm is then used to infer the probability of direction and
absence for the edges in the network.
References:
Martin and Fu (2019) <arXiv:1909.10678>.
Author: Evan A Martin [aut, cre], Audrey Qiuyan Fu [aut]
Maintainer: Evan A Martin <evanamartin@gmail.com>
Diff between baycn versions 1.1.0 dated 2020-03-10 and 1.2.0 dated 2020-07-31
baycn-1.1.0/baycn/R/cll.R |only baycn-1.1.0/baycn/R/lookUp.R |only baycn-1.1.0/baycn/R/lull.R |only baycn-1.1.0/baycn/R/parentCombinations.R |only baycn-1.1.0/baycn/man/directedAM.Rd |only baycn-1.1.0/baycn/man/figures/logo.png |only baycn-1.1.0/baycn/man/plot-baycn-ANY-method.Rd |only baycn-1.2.0/baycn/DESCRIPTION | 10 baycn-1.2.0/baycn/MD5 | 59 baycn-1.2.0/baycn/NAMESPACE | 5 baycn-1.2.0/baycn/R/cPrior.R | 2 baycn-1.2.0/baycn/R/caRatio.R | 5 baycn-1.2.0/baycn/R/carPrior.R | 45 baycn-1.2.0/baycn/R/creation.R | 89 - baycn-1.2.0/baycn/R/cycles.R | 2 baycn-1.2.0/baycn/R/data.R | 44 baycn-1.2.0/baycn/R/directedAM.R | 48 baycn-1.2.0/baycn/R/likelihood.R |only baycn-1.2.0/baycn/R/methods.R | 116 - baycn-1.2.0/baycn/R/mhEdge.R | 116 - baycn-1.2.0/baycn/R/mse.R |only baycn-1.2.0/baycn/R/prerec.R | 136 + baycn-1.2.0/baycn/R/simdata.R | 1803 ++++++++++++++++++++++-- baycn-1.2.0/baycn/R/tracePlot.R |only baycn-1.2.0/baycn/data/drosophila.RData |only baycn-1.2.0/baycn/inst/testdata/baycn_gn4.RData |only baycn-1.2.0/baycn/man/drosophila.Rd |only baycn-1.2.0/baycn/man/figures/baycn_logo.png |only baycn-1.2.0/baycn/man/figures/gn4_mec.jpg |only baycn-1.2.0/baycn/man/figures/gn4_mec.pdf |only baycn-1.2.0/baycn/man/geuvadis.Rd | 6 baycn-1.2.0/baycn/man/mhEdge.Rd | 61 baycn-1.2.0/baycn/man/mse.Rd |only baycn-1.2.0/baycn/man/plot-baycn-method.Rd |only baycn-1.2.0/baycn/man/prerec.Rd | 60 baycn-1.2.0/baycn/man/simdata.Rd | 49 baycn-1.2.0/baycn/man/tracePlot.Rd |only baycn-1.2.0/baycn/tests/testthat/testCLL.R | 97 - baycn-1.2.0/baycn/tests/testthat/testGVCPh.R | 9 baycn-1.2.0/baycn/tests/testthat/testMSE.R |only baycn-1.2.0/baycn/tests/testthat/testPreRec.R |only 41 files changed, 2314 insertions(+), 448 deletions(-)
Title: Download, Compile and Link 'OpenBLAS' Library with R
Description: The 'ropenblas' package (<https://prdm0.github.io/ropenblas/>) is useful for users of any 'GNU/Linux' distribution. It will be possible to download, compile and link the 'OpenBLAS' library (<https://www.openblas.net/>) with the R language, always by the same procedure, regardless of the 'GNU/Linux' distribution used. With the 'ropenblas' package it is possible to download, compile and link the latest version of the 'OpenBLAS' library even the repositories of the 'GNU/Linux' distribution used do not include the latest versions of 'OpenBLAS'. If of interest, older versions of the 'OpenBLAS' library may be considered. Linking R with an optimized version of 'BLAS' (<http://www.netlib.org/blas/>) may improve the computational performance of R code. The 'OpenBLAS' library is an optimized implementation of 'BLAS' that can be easily linked to R with the 'ropenblas' package.
Author: Pedro Rafael D. Marinho [aut, cre]
Maintainer: Pedro Rafael D. Marinho <pedro.rafael.marinho@gmail.com>
Diff between ropenblas versions 0.2.6 dated 2020-05-23 and 0.2.7 dated 2020-07-31
DESCRIPTION | 10 - MD5 | 11 +- NAMESPACE | 3 NEWS.md | 10 + R/ropenblas.R | 288 ++++++++++++++++++++++++++++--------------------------- man/rcompiler.Rd | 2 man/rnews.Rd |only 7 files changed, 174 insertions(+), 150 deletions(-)
Title: Simulates SPSO and Efftox Phase 12 Trials with Correlated
Outcomes
Description: Simulating and conducting four phase 12 clinical trials with correlated binary bivariate outcomes described. Uses the 'Efftox' (efficacy and toxicity tradeoff, <https://biostatistics.mdanderson.org/SoftwareDownload/SingleSoftware/Index/2>) and SPSO (Semi-Parametric Stochastic Ordering) models with Utility and Desirability based objective functions for dose finding.
Author: Andrew G Chapple
Maintainer: Andrew G Chapple <achapp@lsuhsc.edu>
Diff between Phase12Compare versions 1.3 dated 2019-10-02 and 1.5 dated 2020-07-31
DESCRIPTION | 8 - MD5 | 38 ++++---- NAMESPACE | 58 ++++++------ R/RcppExports.R | 8 + man/AssignEffTox.Rd | 133 +++++++++++++++------------- man/AssignEffToxUT.Rd | 87 ++++++++++-------- man/GETBIN.Rd | 34 +++---- man/GetEfftoxContour.Rd | 18 +++ man/GetEfftoxUt.Rd | 18 +++ man/GetSpsoContour.Rd | 18 +++ man/GetSpsoUt.Rd | 18 +++ man/ReturnOpt.Rd | 38 ++++---- man/RunAdaptiveEffToxTrialCORR.Rd | 97 +++++++++++--------- man/RunAdaptiveEffToxTrialCORRCONTOUR.Rd | 97 +++++++++++--------- man/SimEfftoxContour.Rd | 18 +++ man/SimEfftoxUt.Rd | 18 +++ man/SimSpsoContour.Rd | 18 +++ man/SimSpsoUt.Rd | 18 +++ src/RcppExports.cpp | 26 +++++ src/SPSOCODE.cpp | 144 ++++++++++++++++++++----------- 20 files changed, 576 insertions(+), 336 deletions(-)
More information about Phase12Compare at CRAN
Permanent link
Title: Distance Sampling Detection Function and Abundance Estimation
Description: A simple way of fitting detection functions to distance sampling
data for both line and point transects. Adjustment term selection, left and
right truncation as well as monotonicity constraints and binning are
supported. Abundance and density estimates can also be calculated (via a
Horvitz-Thompson-like estimator) if survey area information is provided.
Author: David Lawrence Miller
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between Distance versions 1.0.0 dated 2020-01-31 and 1.0.1 dated 2020-07-31
DESCRIPTION | 11 - MD5 | 77 ++++---- NAMESPACE | 3 NEWS | 213 +++++++++++++---------- R/ER_var_f.R | 68 +++---- R/add_df_covar_line.R |only R/bootdht.R | 51 ++++- R/checkdata.R | 54 +++-- R/dht2.R | 395 +++++++++++++++++++++++++++---------------- R/dht2_checkdata.R | 21 ++ R/dht2_misc.R |only R/ds.R | 57 +++--- R/dsdata.R | 23 ++ R/p_dist_table.R |only R/plot.dsmodel.R | 1 R/predict.dsmodel.R |only R/safe_factorize.R |only R/summary.dht_bootstrap.R | 4 R/varNhat.R | 40 ---- README.md | 1 data/DuikerCameraTraps.RData |only man/ClusterExercise.Rd | 6 man/CueCountingExample.Rd | 6 man/DuikerCameraTraps.Rd |only man/ETP_Dolphin.Rd | 6 man/LTExercise.Rd | 6 man/PTExercise.Rd | 6 man/Savannah_sparrow_1980.Rd | 6 man/Stratify_example.Rd | 6 man/Systematic_variance_1.Rd | 6 man/add_df_covar_line.Rd |only man/amakihi.Rd | 6 man/bootdht.Rd | 10 - man/capercaillie.Rd | 6 man/dht2.Rd | 49 ++++- man/ds.Rd | 30 ++- man/ducknest.Rd | 6 man/golftees.Rd | 6 man/minke.Rd | 6 man/p_dist_table.Rd |only man/plot.dsmodel.Rd | 3 man/predict.dsmodel.Rd |only man/safe_factorize.Rd |only man/sikadeer.Rd | 6 man/unimak.Rd | 6 45 files changed, 749 insertions(+), 452 deletions(-)
Title: Mark-Recapture Distance Sampling
Description: Animal abundance estimation via conventional, multiple covariate
and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function
fitting is performed via maximum likelihood. Also included are diagnostics
and plotting for fitted detection functions. Abundance estimation is via a
Horvitz-Thompson-like estimator.
Author: Jeff Laake <jeff.laake@noaa.gov>, David Borchers
<dlb@st-and.ac.uk>, Len Thomas <len.thomas@st-and.ac.uk>, David
Miller <dave@ninepointeightone.net> and Jon Bishop
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between mrds versions 2.2.2 dated 2020-05-12 and 2.2.3 dated 2020-07-31
DESCRIPTION | 13 +++++++------ MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 1 + NEWS | 7 +++++++ R/add_df_covar_line.R | 1 + R/ddf.ds.R | 5 +++++ R/ddf.gof.R | 5 +++++ R/dht.R | 35 ++++++++++++++++++++++++----------- R/dht.se.R | 2 +- R/p_dist_table.R | 1 + R/sethazard.R | 4 ++-- R/setinitial.ds.R | 19 +++++++------------ R/varn.R | 5 +---- README.md | 9 ++------- man/dht.Rd | 2 +- man/setinitial.ds.Rd | 10 +++++----- man/varn.Rd | 2 +- 17 files changed, 87 insertions(+), 66 deletions(-)
Title: Affine Invariant Tests of Multivariate Normality
Description: Various affine invariant multivariate normality tests are provided. It is designed to accompany the survey article Ebner, B. and Henze, N. (2020) <arXiv:2004.07332> titled "Tests for multivariate normality -- a critical review with emphasis on weighted L^2-statistics". We implement new and time honoured L^2-type tests of multivariate normality, such as the Baringhaus-Henze-Epps-Pulley (BHEP) test, the Henze-Zirkler test, the test of Henze-Jiménes-Gamero, the test of Henze-Jiménes-Gamero-Meintanis, the test of Henze-Visage, the Dörr-Ebner-Henze test based on harmonic oscillator and the Dörr-Ebner-Henze test based on a double estimation in a PDE. Secondly, we include the measures of multivariate skewness and kurtosis by Mardia, Koziol, Malkovich and Afifi and Móri, Rohatgi and Székely, as well as the associated tests. Thirdly, we include the tests of multivariate normality by Cox and Small, the 'energy' test of Székely and Rizzo, the tests based on spherical harmonics by Manzotti and Quiroz and the test of Pudelko. All the functions and tests need the data to be a n x d matrix where n is the samplesize (number of rows) and d is the dimension (number of columns).
Author: Lucas Butsch [aut],
Bruno Ebner [aut, cre],
Jaco Visagie [ctb],
Johann Siemens [ctb]
Maintainer: Bruno Ebner <bruno.ebner@kit.edu>
Diff between mnt versions 1.2 dated 2020-04-25 and 1.3 dated 2020-07-31
DESCRIPTION | 6 +-- MD5 | 92 +++++++++++++++++++++++++------------------------ NAMESPACE | 4 +- R/multNormTest.R | 51 ++++++++++++++++++++++++++- R/teststatistics.R | 55 ++++++++++++++++++++++++++++- man/BHEP.Rd | 66 +++++++++++++++++------------------ man/CS.Rd | 68 ++++++++++++++++++------------------ man/DEHT.Rd | 62 ++++++++++++++++----------------- man/DEHU.Rd | 54 ++++++++++++++--------------- man/EHS.Rd |only man/HJG.Rd | 62 ++++++++++++++++----------------- man/HJM.Rd | 62 ++++++++++++++++----------------- man/HV.Rd | 68 ++++++++++++++++++------------------ man/HZ.Rd | 60 ++++++++++++++++---------------- man/KKurt.Rd | 60 ++++++++++++++++---------------- man/MAKurt.Rd | 68 ++++++++++++++++++------------------ man/MASkew.Rd | 68 ++++++++++++++++++------------------ man/MQ1.Rd | 48 +++++++++++++------------- man/MQ2.Rd | 48 +++++++++++++------------- man/MRSSkew.Rd | 56 +++++++++++++++--------------- man/MSkew.Rd | 64 +++++++++++++++++----------------- man/PU.Rd | 58 +++++++++++++++---------------- man/Quantile09.Rd | 54 ++++++++++++++--------------- man/Quantile095.Rd | 54 ++++++++++++++--------------- man/Quantile099.Rd | 54 ++++++++++++++--------------- man/SR.Rd | 60 ++++++++++++++++---------------- man/cv.quan.Rd | 76 ++++++++++++++++++++--------------------- man/print.mnt.Rd | 54 ++++++++++++++--------------- man/standard.Rd | 32 ++++++++--------- man/test.BHEP.Rd | 88 +++++++++++++++++++++++------------------------ man/test.CS.Rd | 92 ++++++++++++++++++++++++------------------------- man/test.DEHT.Rd | 90 ++++++++++++++++++++++++------------------------ man/test.DEHU.Rd | 90 ++++++++++++++++++++++++------------------------ man/test.EHS.Rd |only man/test.HJG.Rd | 88 +++++++++++++++++++++++------------------------ man/test.HJM.Rd | 90 ++++++++++++++++++++++++------------------------ man/test.HV.Rd | 96 ++++++++++++++++++++++++++-------------------------- man/test.HZ.Rd | 80 +++++++++++++++++++++---------------------- man/test.KKurt.Rd | 84 ++++++++++++++++++++++----------------------- man/test.MAKurt.Rd | 96 ++++++++++++++++++++++++++-------------------------- man/test.MASkew.Rd | 96 ++++++++++++++++++++++++++-------------------------- man/test.MKurt.Rd | 88 +++++++++++++++++++++++------------------------ man/test.MQ1.Rd | 74 ++++++++++++++++++++-------------------- man/test.MQ2.Rd | 72 +++++++++++++++++++-------------------- man/test.MRSSkew.Rd | 88 +++++++++++++++++++++++------------------------ man/test.MSkew.Rd | 88 +++++++++++++++++++++++------------------------ man/test.PU.Rd | 86 +++++++++++++++++++++++----------------------- man/test.SR.Rd | 76 ++++++++++++++++++++--------------------- 48 files changed, 1611 insertions(+), 1515 deletions(-)
Title: Antimicrobial Resistance Analysis
Description: Functions to simplify the analysis and prediction of Antimicrobial
Resistance (AMR) and to work with microbial and antimicrobial properties by
using evidence-based methods, like those defined by Leclercq et al. (2013)
<doi:10.1111/j.1469-0691.2011.03703.x> and the Clinical and Laboratory
Standards Institute (2014) <isbn: 1-56238-899-1>.
Author: Matthijs S. Berends [aut, cre]
(<https://orcid.org/0000-0001-7620-1800>),
Christian F. Luz [aut, ctb] (<https://orcid.org/0000-0001-5809-5995>),
Alexander W. Friedrich [aut, ths]
(<https://orcid.org/0000-0003-4881-038X>),
Bhanu N. M. Sinha [aut, ths] (<https://orcid.org/0000-0003-1634-0010>),
Casper J. Albers [aut, ths] (<https://orcid.org/0000-0002-9213-6743>),
Corinna Glasner [aut, ths] (<https://orcid.org/0000-0003-1241-1328>),
Judith M. Fonville [ctb],
Erwin E. A. Hassing [ctb],
Eric H. L. C. M. Hazenberg [ctb],
Annick Lenglet [ctb],
Bart C. Meijer [ctb],
Sofia Ny [ctb],
Dennis Souverein [ctb]
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>
Diff between AMR versions 1.2.0 dated 2020-05-28 and 1.3.0 dated 2020-07-31
AMR-1.2.0/AMR/inst/doc/AMR.R |only AMR-1.2.0/AMR/inst/doc/AMR.Rmd |only AMR-1.2.0/AMR/inst/doc/AMR.html |only AMR-1.2.0/AMR/inst/doc/EUCAST.R |only AMR-1.2.0/AMR/inst/doc/EUCAST.Rmd |only AMR-1.2.0/AMR/inst/doc/EUCAST.html |only AMR-1.2.0/AMR/inst/doc/MDR.R |only AMR-1.2.0/AMR/inst/doc/MDR.Rmd |only AMR-1.2.0/AMR/inst/doc/MDR.html |only AMR-1.2.0/AMR/inst/doc/PCA.R |only AMR-1.2.0/AMR/inst/doc/PCA.Rmd |only AMR-1.2.0/AMR/inst/doc/PCA.html |only AMR-1.2.0/AMR/inst/doc/WHONET.R |only AMR-1.2.0/AMR/inst/doc/WHONET.Rmd |only AMR-1.2.0/AMR/inst/doc/WHONET.html |only AMR-1.2.0/AMR/inst/doc/resistance_predict.R |only AMR-1.2.0/AMR/inst/doc/resistance_predict.Rmd |only AMR-1.2.0/AMR/inst/doc/resistance_predict.html |only AMR-1.2.0/AMR/tests/testthat/test-mo_history.R |only AMR-1.2.0/AMR/vignettes/AMR.Rmd |only AMR-1.2.0/AMR/vignettes/EUCAST.Rmd |only AMR-1.2.0/AMR/vignettes/MDR.Rmd |only AMR-1.2.0/AMR/vignettes/PCA.Rmd |only AMR-1.2.0/AMR/vignettes/WHONET.Rmd |only AMR-1.2.0/AMR/vignettes/resistance_predict.Rmd |only AMR-1.3.0/AMR/DESCRIPTION | 14 AMR-1.3.0/AMR/MD5 | 297 +++---- AMR-1.3.0/AMR/NAMESPACE | 17 AMR-1.3.0/AMR/NEWS.md | 69 + AMR-1.3.0/AMR/R/aa_helper_functions.R | 206 +++-- AMR-1.3.0/AMR/R/aa_helper_functions_dplyr.R | 4 AMR-1.3.0/AMR/R/ab.R | 410 ++++++---- AMR-1.3.0/AMR/R/ab_class_selectors.R |only AMR-1.3.0/AMR/R/ab_from_text.R |only AMR-1.3.0/AMR/R/ab_property.R | 21 AMR-1.3.0/AMR/R/age.R | 38 AMR-1.3.0/AMR/R/amr.R | 33 AMR-1.3.0/AMR/R/atc_online.R | 70 - AMR-1.3.0/AMR/R/availability.R | 15 AMR-1.3.0/AMR/R/bug_drug_combinations.R | 39 AMR-1.3.0/AMR/R/catalogue_of_life.R | 10 AMR-1.3.0/AMR/R/count.R | 6 AMR-1.3.0/AMR/R/data.R | 28 AMR-1.3.0/AMR/R/deprecated.R | 4 AMR-1.3.0/AMR/R/disk.R | 12 AMR-1.3.0/AMR/R/eucast_rules.R | 51 - AMR-1.3.0/AMR/R/filter_ab_class.R | 150 ++- AMR-1.3.0/AMR/R/first_isolate.R | 163 +-- AMR-1.3.0/AMR/R/g.test.R | 4 AMR-1.3.0/AMR/R/ggplot_pca.R | 89 +- AMR-1.3.0/AMR/R/ggplot_rsi.R | 37 AMR-1.3.0/AMR/R/globals.R | 60 - AMR-1.3.0/AMR/R/guess_ab_col.R | 58 - AMR-1.3.0/AMR/R/join_microorganisms.R | 49 + AMR-1.3.0/AMR/R/key_antibiotics.R | 86 +- AMR-1.3.0/AMR/R/kurtosis.R | 4 AMR-1.3.0/AMR/R/lifecycle.R | 12 AMR-1.3.0/AMR/R/like.R | 29 AMR-1.3.0/AMR/R/mdro.R | 95 +- AMR-1.3.0/AMR/R/mic.R | 21 AMR-1.3.0/AMR/R/mo.R | 120 +- AMR-1.3.0/AMR/R/mo_property.R | 81 + AMR-1.3.0/AMR/R/mo_source.R | 50 - AMR-1.3.0/AMR/R/p_symbol.R | 8 AMR-1.3.0/AMR/R/pca.R | 9 AMR-1.3.0/AMR/R/proportion.R | 8 AMR-1.3.0/AMR/R/resistance_predict.R | 113 +- AMR-1.3.0/AMR/R/rsi.R | 217 ++--- AMR-1.3.0/AMR/R/rsi_calc.R | 146 ++- AMR-1.3.0/AMR/R/rsi_df.R | 4 AMR-1.3.0/AMR/R/skewness.R | 4 AMR-1.3.0/AMR/R/sysdata.rda |binary AMR-1.3.0/AMR/R/translate.R | 25 AMR-1.3.0/AMR/R/whocc.R | 4 AMR-1.3.0/AMR/R/zzz.R | 221 ----- AMR-1.3.0/AMR/README.md | 16 AMR-1.3.0/AMR/build/vignette.rds |binary AMR-1.3.0/AMR/data/antibiotics.rda |binary AMR-1.3.0/AMR/data/microorganisms.rda |binary AMR-1.3.0/AMR/data/rsi_translation.rda |binary AMR-1.3.0/AMR/inst/doc/welcome_to_AMR.R |only AMR-1.3.0/AMR/inst/doc/welcome_to_AMR.Rmd |only AMR-1.3.0/AMR/inst/doc/welcome_to_AMR.html |only AMR-1.3.0/AMR/man/AMR-deprecated.Rd | 4 AMR-1.3.0/AMR/man/AMR.Rd | 25 AMR-1.3.0/AMR/man/WHOCC.Rd | 2 AMR-1.3.0/AMR/man/WHONET.Rd | 2 AMR-1.3.0/AMR/man/ab_from_text.Rd |only AMR-1.3.0/AMR/man/ab_property.Rd | 6 AMR-1.3.0/AMR/man/age.Rd | 4 AMR-1.3.0/AMR/man/age_groups.Rd | 4 AMR-1.3.0/AMR/man/antibiotic_class_selectors.Rd |only AMR-1.3.0/AMR/man/antibiotics.Rd | 14 AMR-1.3.0/AMR/man/as.ab.Rd | 21 AMR-1.3.0/AMR/man/as.disk.Rd | 4 AMR-1.3.0/AMR/man/as.mic.Rd | 4 AMR-1.3.0/AMR/man/as.mo.Rd | 30 AMR-1.3.0/AMR/man/as.rsi.Rd | 40 AMR-1.3.0/AMR/man/atc_online.Rd | 4 AMR-1.3.0/AMR/man/availability.Rd | 4 AMR-1.3.0/AMR/man/bug_drug_combinations.Rd | 4 AMR-1.3.0/AMR/man/catalogue_of_life.Rd | 4 AMR-1.3.0/AMR/man/catalogue_of_life_version.Rd | 2 AMR-1.3.0/AMR/man/count.Rd | 6 AMR-1.3.0/AMR/man/eucast_rules.Rd | 6 AMR-1.3.0/AMR/man/example_isolates.Rd | 4 AMR-1.3.0/AMR/man/example_isolates_unclean.Rd | 2 AMR-1.3.0/AMR/man/filter_ab_class.Rd | 23 AMR-1.3.0/AMR/man/first_isolate.Rd | 4 AMR-1.3.0/AMR/man/g.test.Rd | 4 AMR-1.3.0/AMR/man/ggplot_pca.Rd | 35 AMR-1.3.0/AMR/man/ggplot_rsi.Rd | 14 AMR-1.3.0/AMR/man/guess_ab_col.Rd | 6 AMR-1.3.0/AMR/man/join.Rd | 8 AMR-1.3.0/AMR/man/key_antibiotics.Rd | 4 AMR-1.3.0/AMR/man/kurtosis.Rd | 4 AMR-1.3.0/AMR/man/lifecycle.Rd | 16 AMR-1.3.0/AMR/man/like.Rd | 4 AMR-1.3.0/AMR/man/mdro.Rd | 6 AMR-1.3.0/AMR/man/microorganisms.Rd | 18 AMR-1.3.0/AMR/man/microorganisms.codes.Rd | 2 AMR-1.3.0/AMR/man/microorganisms.old.Rd | 2 AMR-1.3.0/AMR/man/mo_property.Rd | 21 AMR-1.3.0/AMR/man/mo_source.Rd | 4 AMR-1.3.0/AMR/man/p_symbol.Rd | 4 AMR-1.3.0/AMR/man/pca.Rd | 2 AMR-1.3.0/AMR/man/proportion.Rd | 10 AMR-1.3.0/AMR/man/resistance_predict.Rd | 8 AMR-1.3.0/AMR/man/rsi_translation.Rd | 6 AMR-1.3.0/AMR/man/skewness.Rd | 4 AMR-1.3.0/AMR/man/translate.Rd | 10 AMR-1.3.0/AMR/tests/testthat.R | 4 AMR-1.3.0/AMR/tests/testthat/Rplots.pdf |binary AMR-1.3.0/AMR/tests/testthat/test-ab.R | 15 AMR-1.3.0/AMR/tests/testthat/test-ab_from_text.R |only AMR-1.3.0/AMR/tests/testthat/test-ab_property.R | 7 AMR-1.3.0/AMR/tests/testthat/test-age.R | 6 AMR-1.3.0/AMR/tests/testthat/test-antibiotic_class_selectors.R |only AMR-1.3.0/AMR/tests/testthat/test-availability.R | 5 AMR-1.3.0/AMR/tests/testthat/test-bug_drug_combinations.R | 5 AMR-1.3.0/AMR/tests/testthat/test-count.R | 25 AMR-1.3.0/AMR/tests/testthat/test-data.R | 26 AMR-1.3.0/AMR/tests/testthat/test-deprecated.R | 5 AMR-1.3.0/AMR/tests/testthat/test-disk.R | 5 AMR-1.3.0/AMR/tests/testthat/test-eucast_rules.R | 4 AMR-1.3.0/AMR/tests/testthat/test-filter_ab_class.R | 4 AMR-1.3.0/AMR/tests/testthat/test-first_isolate.R | 5 AMR-1.3.0/AMR/tests/testthat/test-g.test.R | 5 AMR-1.3.0/AMR/tests/testthat/test-get_locale.R | 5 AMR-1.3.0/AMR/tests/testthat/test-ggplot_rsi.R | 6 AMR-1.3.0/AMR/tests/testthat/test-guess_ab_col.R | 5 AMR-1.3.0/AMR/tests/testthat/test-join_microorganisms.R | 9 AMR-1.3.0/AMR/tests/testthat/test-key_antibiotics.R | 5 AMR-1.3.0/AMR/tests/testthat/test-kurtosis.R | 5 AMR-1.3.0/AMR/tests/testthat/test-like.R | 5 AMR-1.3.0/AMR/tests/testthat/test-mdro.R | 4 AMR-1.3.0/AMR/tests/testthat/test-mic.R | 5 AMR-1.3.0/AMR/tests/testthat/test-misc.R | 7 AMR-1.3.0/AMR/tests/testthat/test-mo.R | 17 AMR-1.3.0/AMR/tests/testthat/test-mo_property.R | 7 AMR-1.3.0/AMR/tests/testthat/test-p_symbol.R | 5 AMR-1.3.0/AMR/tests/testthat/test-pca.R | 8 AMR-1.3.0/AMR/tests/testthat/test-proportion.R | 7 AMR-1.3.0/AMR/tests/testthat/test-resistance_predict.R | 5 AMR-1.3.0/AMR/tests/testthat/test-rsi.R | 24 AMR-1.3.0/AMR/tests/testthat/test-skewness.R | 5 AMR-1.3.0/AMR/vignettes/welcome_to_AMR.Rmd |only 167 files changed, 2040 insertions(+), 1857 deletions(-)
Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include 'Microsoft Sql Server', 'Oracle',
'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', and 'SQLite'.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.6.6 dated 2020-05-19 and 1.6.8 dated 2020-07-31
DESCRIPTION | 10 ++--- MD5 | 22 +++++------ NEWS.md | 22 +++++++++++ R/HelperFunctions.R | 3 + R/RenderSql.R | 38 +++++++++++++------ build/vignette.rds |binary inst/csv/replacementPatterns.csv | 30 +++++++-------- inst/doc/UsingSqlRender.pdf |binary man/renderSql.Rd | 48 ++++++++++++------------ man/translate.Rd | 64 ++++++++++++++++----------------- man/translateSql.Rd | 48 ++++++++++++------------ tests/testthat/test-translate-sqlite.R | 10 +---- 12 files changed, 165 insertions(+), 130 deletions(-)
Title: Tools for Model Specification in the Latent Variable Framework
Description: Tools for model specification in the latent variable framework
(add-on to the 'lava' package). The package contains three main functionalities:
Wald tests/F-tests with improved control of the type 1 error in small samples,
adjustment for multiple comparisons when searching for local dependencies,
and adjustment for multiple comparisons when doing inference for multiple latent variable models.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>)
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between lavaSearch2 versions 1.5.5 dated 2020-03-18 and 1.5.6 dated 2020-07-31
DESCRIPTION | 15 MD5 | 148 - NAMESPACE | 504 +-- NEWS | 166 - R/0onload.R | 9 R/RcppExports.R | 26 R/calcDistMax.R | 5 R/getVarCov2.R | 19 R/iid2.R | 2 R/information2.R | 2 R/modelsearch2.R | 308 +- R/multcomp.R | 16 R/nobs.R | 9 R/sCorrect.R | 2 R/score2.R | 2 R/summary.modelsearch2.R | 10 R/vcov2.R | 2 build/vignette.rds |binary inst/doc/overview.ltx | 2376 +++++++++--------- inst/doc/overview.pdf |binary inst/implementationScheme.png |only inst/implementationScheme.svg |only inst/likelihood-derivatives-LVM |only man/addLink.Rd | 11 man/autoplot.intDensTri.Rd | 3 man/autoplot.modelsearch2.Rd | 13 man/autoplot_calibrateType1.Rd | 17 man/calcDistMax.Rd | 35 man/calcType1postSelection.Rd | 13 man/calibrateType1.Rd | 49 man/clean.Rd | 3 man/coefByType.Rd | 3 man/compare2.Rd | 23 man/conditionalMoment.Rd | 45 man/createContrast.Rd | 19 man/dInformation2-internal.Rd | 16 man/effects2.Rd | 3 man/estimate2.Rd | 18 man/evalInParentEnv.Rd | 32 man/extractData.Rd | 58 man/findNewLink.Rd | 14 man/getIndexOmega2-internal.Rd | 22 man/getStep.Rd | 3 man/getVarCov2-internal.Rd | 11 man/getVarCov2.Rd | 4 man/glht2.Rd | 22 man/iid2.Rd | 28 man/iidJack.Rd | 14 man/information2-internal.Rd | 39 man/initVarLink.Rd | 9 man/intDensTri.Rd | 14 man/matrixPower.Rd | 3 man/modelsearch2.Rd | 49 man/residuals2.Rd | 12 man/sCorrect.Rd | 83 man/score2-internal.Rd | 15 man/score2.Rd | 12 man/skeleton.Rd | 109 man/summary.calibrateType1.Rd | 13 man/summary2.Rd | 37 man/validFCTs.Rd | 124 man/vcov2.Rd | 12 src/RcppExports.cpp | 17 src/wildBoot.cpp |only tests/testthat/test1-Utils-nlme.R | 4 tests/testthat/test1-adjustMoment.R | 6 tests/testthat/test1-compare2.R | 18 tests/testthat/test1-sCorrect-smallSampleCorrection.R | 56 tests/testthat/test1-sCorrect-validObjects.R | 227 - tests/testthat/test2-modelsearch2.R | 35 vignettes/changes.sty | 1054 +++---- vignettes/overview.ltx | 2376 +++++++++--------- vignettes/overview.org | 2148 ++++++++-------- 73 files changed, 5648 insertions(+), 4924 deletions(-)
Title: Transformation Models with Mixed Effects
Description: Likelihood-based estimation of mixed-effects transformation models using the Template
Model Builder (TMB). The technical details of transformation models are given in Hothorn et al. (2018)
<doi:10.1111/sjos.12291>. The random effects are assumed to be normally distributed on the scale of the
transformation function, the marginal likelihood is evaluated using the Laplace approximation,
and the gradients are calculated with automatic differentiation (AD).
Author: Balint Tamasi [aut, cre] (<https://orcid.org/0000-0002-2629-7362>),
Torsten Hothorn [ctb] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Balint Tamasi <balint.tamasi@uzh.ch>
Diff between tramME versions 0.0.2 dated 2020-04-07 and 0.0.3 dated 2020-07-31
DESCRIPTION | 13 +- MD5 | 72 ++++++------- NEWS.md | 6 + build/vignette.rds |binary inst/doc/tramME.R | 6 - inst/doc/tramME.Rnw | 4 inst/doc/tramME.pdf |binary man/BoxCoxME.Rd | 19 ++- man/ColrME.Rd | 19 ++- man/CoxphME.Rd | 19 ++- man/LehmannME.Rd | 19 ++- man/LmME.Rd | 19 ++- man/PolrME.Rd | 21 ++- man/SurvregME.Rd | 24 +++- man/confint.LmME.Rd | 15 ++ man/confint.tramME.Rd | 15 ++ man/dot-paridx.Rd | 3 man/plot.trafo.tramME.Rd | 3 man/print.VarCorr.tramME.Rd | 3 man/print.anova.tramME.Rd | 8 + man/print.summary.tramME.Rd | 8 + man/print.tramME.Rd | 3 man/simulate.tramME.Rd | 13 +- man/trafo.tramME.Rd | 12 +- man/variable.names.tramME.Rd | 7 - man/vcov.LmME.Rd | 9 + man/vcov.tramME.Rd | 9 + tests/LmME.R | 3 tests/LmME.Rout.save | 10 - tests/basics.R | 36 ++++-- tests/basics.Rout.save | 230 +++++++++++++------------------------------ tests/methods.R | 5 tests/methods.Rout.save | 15 +- tests/predict.Rout.save | 6 - tests/simulate.Rout.save | 6 - tests/test_util.R |only tests/test_util.Rout.save |only vignettes/tramME.Rnw | 4 38 files changed, 355 insertions(+), 309 deletions(-)
Title: Representative and Adequate Prioritization Toolkit in R
Description: Biodiversity is in crisis. The overarching aim of conservation
is to preserve biodiversity patterns and processes. To this end, protected
areas are established to buffer species and preserve biodiversity processes.
But resources are limited and so protected areas must be cost-effective.
This package contains tools to generate plans for protected areas
(prioritizations), using spatially explicit targets for biodiversity
patterns and processes. To obtain solutions in a feasible amount of time,
this package uses the commercial 'Gurobi' software package (obtained from
<http://www.gurobi.com/>). For more information on using
this package, see Hanson et al. (2018) <doi:10.1111/2041-210X.12862>.
Author: Jeffrey O Hanson [aut, cre],
Jonathan R Rhodes [aut],
Hugh P Possingham [aut],
Richard A Fuller [aut]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between raptr versions 0.1.6 dated 2020-03-11 and 0.1.7 dated 2020-07-31
raptr-0.1.6/raptr/data/datalist |only raptr-0.1.6/raptr/man/is.gdalInstalled.Rd |only raptr-0.1.6/raptr/man/rasterizeGDAL.Rd |only raptr-0.1.7/raptr/DESCRIPTION | 18 raptr-0.1.7/raptr/MD5 | 216 +++---- raptr-0.1.7/raptr/NAMESPACE | 4 raptr-0.1.7/raptr/NEWS.md | 31 - raptr-0.1.7/raptr/R/AttributeSpace.R | 22 raptr-0.1.7/raptr/R/AttributeSpaces.R | 14 raptr-0.1.7/raptr/R/DemandPoints.R | 46 - raptr-0.1.7/raptr/R/GurobiOpts.R | 72 +- raptr-0.1.7/raptr/R/ManualOpts.R | 10 raptr-0.1.7/raptr/R/PlanningUnitPoints.R | 14 raptr-0.1.7/raptr/R/RapData.R | 136 ++-- raptr-0.1.7/raptr/R/RapReliableOpts.R | 18 raptr-0.1.7/raptr/R/RapResults.R | 62 +- raptr-0.1.7/raptr/R/RapSolved.R | 36 - raptr-0.1.7/raptr/R/RapUnreliableOpts.R | 8 raptr-0.1.7/raptr/R/RapUnsolved.R | 26 raptr-0.1.7/raptr/R/calcBoundaryData.R | 30 - raptr-0.1.7/raptr/R/calcSpeciesAverageInPus.R | 20 raptr-0.1.7/raptr/R/data.R | 65 -- raptr-0.1.7/raptr/R/dependencies.R | 2 raptr-0.1.7/raptr/R/generics.R | 609 ++++++++++------------ raptr-0.1.7/raptr/R/misc.R | 114 ---- raptr-0.1.7/raptr/R/rap.R | 36 - raptr-0.1.7/raptr/R/raptr-internal.R | 412 +------------- raptr-0.1.7/raptr/R/raptr.R | 27 raptr-0.1.7/raptr/R/rrap.proportion.held.R | 14 raptr-0.1.7/raptr/R/sim.pus.R | 20 raptr-0.1.7/raptr/R/sim.space.R | 2 raptr-0.1.7/raptr/R/sim.species.R | 2 raptr-0.1.7/raptr/R/urap.proportion.held.R | 12 raptr-0.1.7/raptr/README.md | 9 raptr-0.1.7/raptr/build/vignette.rds |binary raptr-0.1.7/raptr/inst/WORDLIST |only raptr-0.1.7/raptr/inst/doc/raptr.Rmd | 4 raptr-0.1.7/raptr/inst/doc/raptr.html | 366 +++++-------- raptr-0.1.7/raptr/man/AttributeSpace-class.Rd | 9 raptr-0.1.7/raptr/man/AttributeSpace.Rd | 8 raptr-0.1.7/raptr/man/AttributeSpaces-class.Rd | 5 raptr-0.1.7/raptr/man/AttributeSpaces.Rd | 4 raptr-0.1.7/raptr/man/DemandPoints-class.Rd | 5 raptr-0.1.7/raptr/man/DemandPoints.Rd | 4 raptr-0.1.7/raptr/man/GurobiOpts-class.Rd | 3 raptr-0.1.7/raptr/man/GurobiOpts.Rd | 16 raptr-0.1.7/raptr/man/ManualOpts-class.Rd | 3 raptr-0.1.7/raptr/man/ManualOpts.Rd | 4 raptr-0.1.7/raptr/man/PlanningUnitPoints-class.Rd | 5 raptr-0.1.7/raptr/man/PlanningUnitPoints.Rd | 4 raptr-0.1.7/raptr/man/PolySet-class.Rd | 3 raptr-0.1.7/raptr/man/RapData-class.Rd | 17 raptr-0.1.7/raptr/man/RapData.Rd | 37 - raptr-0.1.7/raptr/man/RapOpts-class.Rd | 5 raptr-0.1.7/raptr/man/RapReliableOpts-class.Rd | 3 raptr-0.1.7/raptr/man/RapReliableOpts.Rd | 2 raptr-0.1.7/raptr/man/RapResults-class.Rd | 16 raptr-0.1.7/raptr/man/RapResults.Rd | 29 - raptr-0.1.7/raptr/man/RapSolved-class.Rd | 15 raptr-0.1.7/raptr/man/RapSolved.Rd | 14 raptr-0.1.7/raptr/man/RapUnreliableOpts-class.Rd | 1 raptr-0.1.7/raptr/man/RapUnreliableOpts.Rd | 4 raptr-0.1.7/raptr/man/RapUnsolved-class.Rd | 9 raptr-0.1.7/raptr/man/RapUnsolved.Rd | 18 raptr-0.1.7/raptr/man/SolverOpts-class.Rd | 3 raptr-0.1.7/raptr/man/SpatialPolygons2PolySet.Rd | 26 raptr-0.1.7/raptr/man/amount.held.Rd | 16 raptr-0.1.7/raptr/man/amount.target.Rd | 8 raptr-0.1.7/raptr/man/as.list.Rd | 8 raptr-0.1.7/raptr/man/basemap.Rd | 11 raptr-0.1.7/raptr/man/blank.raster.Rd | 4 raptr-0.1.7/raptr/man/cache.Rd | 13 raptr-0.1.7/raptr/man/calcBoundaryData.Rd | 26 raptr-0.1.7/raptr/man/calcSpeciesAverageInPus.Rd | 38 - raptr-0.1.7/raptr/man/casestudy_data.Rd | 21 raptr-0.1.7/raptr/man/dp.subset.Rd | 16 raptr-0.1.7/raptr/man/is.GurobiInstalled.Rd | 6 raptr-0.1.7/raptr/man/is.cached.Rd | 9 raptr-0.1.7/raptr/man/is.comparable.Rd | 7 raptr-0.1.7/raptr/man/logging.file.Rd | 6 raptr-0.1.7/raptr/man/make.DemandPoints.Rd | 43 - raptr-0.1.7/raptr/man/make.RapData.Rd | 38 - raptr-0.1.7/raptr/man/maximum.targets.Rd | 4 raptr-0.1.7/raptr/man/names.Rd | 8 raptr-0.1.7/raptr/man/plot.Rd | 39 - raptr-0.1.7/raptr/man/print.Rd | 16 raptr-0.1.7/raptr/man/prob.subset.Rd | 12 raptr-0.1.7/raptr/man/pu.subset.Rd | 16 raptr-0.1.7/raptr/man/randomPoints.Rd | 8 raptr-0.1.7/raptr/man/rap.Rd | 36 - raptr-0.1.7/raptr/man/raptr.Rd | 28 - raptr-0.1.7/raptr/man/read.RapResults.Rd | 14 raptr-0.1.7/raptr/man/rrap.proportion.held.Rd | 17 raptr-0.1.7/raptr/man/score.Rd | 10 raptr-0.1.7/raptr/man/selections.Rd | 12 raptr-0.1.7/raptr/man/show.Rd | 17 raptr-0.1.7/raptr/man/sim.pus.Rd | 21 raptr-0.1.7/raptr/man/sim.space.Rd | 22 raptr-0.1.7/raptr/man/sim.species.Rd | 40 - raptr-0.1.7/raptr/man/simulated_data.Rd | 21 raptr-0.1.7/raptr/man/solve.Rd | 24 raptr-0.1.7/raptr/man/space.held.Rd | 13 raptr-0.1.7/raptr/man/space.plot.Rd | 44 + raptr-0.1.7/raptr/man/space.target.Rd | 16 raptr-0.1.7/raptr/man/spp.plot.Rd | 60 +- raptr-0.1.7/raptr/man/spp.subset.Rd | 16 raptr-0.1.7/raptr/man/summary.Rd | 14 raptr-0.1.7/raptr/man/update.Rd | 71 +- raptr-0.1.7/raptr/man/urap.proportion.held.Rd | 6 raptr-0.1.7/raptr/tests/testthat/test-02-misc.R | 7 raptr-0.1.7/raptr/vignettes/raptr.Rmd | 4 111 files changed, 1622 insertions(+), 2013 deletions(-)
Title: An Implementation of Two Modern Education-Based Value-Added
Models
Description: Provides functions that fit two modern education-based value-added models.
One of these models is the quantile value-added model. This model
permits estimating a school's value-added based on specific quantiles of
the post-test distribution. Estimating value-added based on quantiles
of the post-test distribution provides a more complete picture of an
education institution's contribution to learning for students of all
abilities. See Page, G.L.; San Martín, E.; Orellana, J.; Gonzalez, J. (2017)
<doi:10.1111/rssa.12195> for more details. The second model is a temporally
dependent value-added model. This model takes into account the temporal
dependence that may exist in school performance between two cohorts in one
of two ways. The first is by modeling school random effects with a
non-stationary AR(1) process. The second is by modeling school effects
based on previous cohort's post-test performance. In addition to more
efficiently estimating value-added, this model permits making statements
about the persistence of a schools effectiveness. The standard value-added
model is also an option.
Author: Garritt L. Page [aut, cre, cph],
S. McKay Curtis [ctb, cph],
Radford M. Neal [ctb, cph]
Maintainer: Garritt L. Page <page@stat.byu.edu>
Diff between modernVA versions 0.1.0 dated 2020-07-18 and 0.1.1 dated 2020-07-31
modernVA-0.1.0/modernVA/src/modernVA_init.c |only modernVA-0.1.1/modernVA/DESCRIPTION | 10 ++++---- modernVA-0.1.1/modernVA/MD5 | 15 +++++------- modernVA-0.1.1/modernVA/R/functions.R | 22 +++++++++--------- modernVA-0.1.1/modernVA/src/init.c | 33 ++++++++++++++++------------ modernVA-0.1.1/modernVA/src/tdVAM2a1.c | 1 modernVA-0.1.1/modernVA/src/tdVAM2a2.c | 1 modernVA-0.1.1/modernVA/src/tdVAM2b1.c | 1 modernVA-0.1.1/modernVA/src/tdVAM2b2.c | 1 9 files changed, 47 insertions(+), 37 deletions(-)
Title: Learning Causal or Non-Causal Graphical Models Using Information
Theory
Description: We report an information-theoretic method which learns a large class of causal or non-causal graphical models from purely observational data, while including the effects of unobserved latent variables, commonly found in many datasets. Starting from a complete graph, the method iteratively removes dispensable edges, by uncovering significant information contributions from indirect paths, and assesses edge-specific confidences from randomization of available data. The remaining edges are then oriented based on the signature of causality in observational data. This approach can be applied on a wide range of datasets and provide new biological insights on regulatory networks from single cell expression data, genomic alterations during tumor development and co-evolving residues in protein structures. For more information you can refer to: Cabeli et al. PLoS Comp. Bio. 2020 <doi:10.1371/journal.pcbi.1007866>, Verny et al. PLoS Comp. Bio. 2017 <doi:10.1371/journal.pcbi.1005662>.
Author: Vincent Cabeli [aut, cre],
Honghao Li [aut],
Marcel Ribeiro Dantas [aut],
Nadir Sella [aut],
Louis Verny [aut],
Severine Affeldt [aut],
Hervé Isambert [aut]
Maintainer: Vincent Cabeli <vincent.cabeli@curie.fr>
Diff between miic versions 1.4.0 dated 2020-07-22 and 1.4.2 dated 2020-07-31
DESCRIPTION | 10 +- MD5 | 37 ++++----- R/miic.reconstruct.R | 21 ----- src/computation_cache.h | 5 - src/compute_ens_information.cpp | 8 - src/compute_info.cpp | 36 ++++---- src/confidence_cut.cpp | 164 ++++++++++++++++------------------------ src/confidence_cut.h |only src/info_cnt.cpp | 52 ++++-------- src/info_cnt.h | 2 src/mutual_information.cpp | 14 +-- src/mutual_information.h | 16 ++- src/orientation_probability.cpp | 4 src/proba_orientation.cpp | 8 + src/reconstruct.cpp | 16 +-- src/reconstruct.h | 1 src/skeleton_initialization.cpp | 12 -- src/skeleton_iteration.cpp | 7 - src/structure.h | 41 ++++++---- src/utilities.cpp | 40 +++++---- 20 files changed, 223 insertions(+), 271 deletions(-)
Title: Open Source Geometry Engine ('GEOS') C API
Description: Provides the Open Source Geometry Engine ('GEOS') as a
C API that can be used to write high-performance C and C++
geometry operations using R as an interface. Headers are provided
to make linking to and using these functions from C++ code as
easy and as safe as possible. This package contains an internal
copy of the 'GEOS' library to guarantee the best possible
consistency on multiple platforms.
Author: Dewey Dunnington [aut, cre] (<https://orcid.org/0000-0002-9415-4582>),
GEOS authors [aut],
Martin Davis [ctb, cph],
Benjamin Campbell [ctb, cph],
Tomasz Sowa [ctb, cph],
Christian Kaiser [ctb, cph],
David Skea [ctb, cph],
Daniel Baston [ctb, cph],
Sandro Santilli [ctb, cph],
Mateusz Loskot [ctb, cph],
Paul Ramsey [ctb, cph],
Olivier Devillers [ctb, cph],
Sean Gillies [ctb, cph],
Mika Heiskanen [ctb, cph],
Safe Software Inc. [cph],
Refractions Research Inc. [cph],
Vivid Solutions Inc. [cph]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between libgeos versions 3.8.1-2 dated 2020-07-21 and 3.8.1-3 dated 2020-07-31
libgeos-3.8.1-2/libgeos/src/libgeos-init.cpp |only libgeos-3.8.1-3/libgeos/DESCRIPTION | 6 libgeos-3.8.1-3/libgeos/MD5 | 15 libgeos-3.8.1-3/libgeos/NEWS.md | 6 libgeos-3.8.1-3/libgeos/R/libgeos-package.R | 2 libgeos-3.8.1-3/libgeos/src/Makevars | 3 libgeos-3.8.1-3/libgeos/src/geos/geos_ts_c.cpp | 30 libgeos-3.8.1-3/libgeos/src/geos_include/geos_c.h | 875 +++++++++++++++++++++- libgeos-3.8.1-3/libgeos/src/libgeos-init.c |only libgeos-3.8.1-3/libgeos/src/libgeos-version.c |only 10 files changed, 891 insertions(+), 46 deletions(-)
Title: Bayesian Regression Models using 'Stan'
Description: Fit Bayesian generalized (non-)linear multivariate multilevel models
using 'Stan' for full Bayesian inference. A wide range of distributions
and link functions are supported, allowing users to fit -- among others --
linear, robust linear, count data, survival, response times, ordinal,
zero-inflated, hurdle, and even self-defined mixture models all in a
multilevel context. Further modeling options include non-linear and
smooth terms, auto-correlation structures, censored data, meta-analytic
standard errors, and quite a few more. In addition, all parameters of the
response distribution can be predicted in order to perform distributional
regression. Prior specifications are flexible and explicitly encourage
users to apply prior distributions that actually reflect their beliefs.
Model fit can easily be assessed and compared with posterior predictive
checks and leave-one-out cross-validation. References: Bürkner (2017)
<doi:10.18637/jss.v080.i01>; Bürkner (2018) <doi:10.32614/RJ-2018-017>;
Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
Author: Paul-Christian Bürkner [aut, cre],
Jonah Gabry [ctb]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>
Diff between brms versions 2.13.3 dated 2020-07-13 and 2.13.5 dated 2020-07-31
DESCRIPTION | 12 MD5 | 90 NAMESPACE | 4 NEWS.md | 4008 +++++++++++++++---------------- R/brmsterms.R | 2108 ++++++++-------- R/data-predictor.R | 1881 +++++++------- R/data-response.R | 1195 ++++----- R/families.R | 3377 +++++++++++++------------- R/family-lists.R | 932 +++---- R/kfold.R | 8 R/log_lik.R | 3 R/loo.R | 426 --- R/loo_moment_match.R |only R/loo_subsample.R |only R/posterior_epred.R | 6 R/posterior_predict.R | 39 R/prepare_predictions.R | 2343 +++++++++--------- R/priors.R | 3857 +++++++++++++++--------------- R/reloo.R |only R/restructure.R | 1393 +++++----- R/stan-predictor.R | 4056 +++++++++++++++---------------- R/stan-response.R | 1141 ++++---- build/vignette.rds |binary inst/chunks/fun_cox.stan | 74 inst/doc/brms_customfamilies.html | 76 inst/doc/brms_distreg.html | 106 inst/doc/brms_families.Rmd | 656 ++--- inst/doc/brms_families.html | 32 inst/doc/brms_missings.html | 62 inst/doc/brms_monotonic.html | 140 - inst/doc/brms_multilevel.pdf |binary inst/doc/brms_multivariate.html | 188 - inst/doc/brms_nonlinear.html | 122 inst/doc/brms_overview.pdf |binary inst/doc/brms_phylogenetics.html | 122 man/brmsfamily.Rd | 13 man/log_lik.brmsfit.Rd | 14 man/loo.brmsfit.Rd | 8 man/loo_moment_match.brmsfit.Rd |only man/loo_subsample.brmsfit.Rd | 2 man/posterior_epred.brmsfit.Rd | 8 man/posterior_predict.brmsfit.Rd | 40 man/reloo.brmsfit.Rd | 4 tests/testthat/tests.brm.R | 122 tests/testthat/tests.brmsfit-methods.R | 1811 +++++++------- tests/testthat/tests.make_stancode.R | 4196 ++++++++++++++++----------------- tests/testthat/tests.make_standata.R | 1883 +++++++------- vignettes/brms_families.Rmd | 656 ++--- 48 files changed, 18621 insertions(+), 18593 deletions(-)
Title: Tidy Messy Data
Description: Tools to help to create tidy data, where each column is a
variable, each row is an observation, and each cell contains a single value.
'tidyr' contains tools for changing the shape (pivoting) and hierarchy
(nesting and 'unnesting') of a dataset, turning deeply nested lists
into rectangular data frames ('rectangling'), and extracting values out
of string columns. It also includes tools for working with missing values
(both implicit and explicit).
Author: Hadley Wickham [aut, cre],
Lionel Henry [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 1.1.0 dated 2020-05-20 and 1.1.1 dated 2020-07-31
tidyr-1.1.0/tidyr/R/RcppExports.R |only tidyr-1.1.0/tidyr/src/RcppExports.cpp |only tidyr-1.1.0/tidyr/tests/testthat/test-pack-name-repair.txt |only tidyr-1.1.1/tidyr/DESCRIPTION | 15 - tidyr-1.1.1/tidyr/MD5 | 77 +++---- tidyr-1.1.1/tidyr/NAMESPACE | 1 tidyr-1.1.1/tidyr/NEWS.md | 11 + tidyr-1.1.1/tidyr/R/cpp11.R |only tidyr-1.1.1/tidyr/R/extract.R | 32 ++- tidyr-1.1.1/tidyr/R/fill.R | 3 tidyr-1.1.1/tidyr/R/pivot-long.R | 2 tidyr-1.1.1/tidyr/R/separate-rows.R | 2 tidyr-1.1.1/tidyr/R/separate.R | 25 ++ tidyr-1.1.1/tidyr/R/utils.R | 2 tidyr-1.1.1/tidyr/build/tidyr.pdf |binary tidyr-1.1.1/tidyr/build/vignette.rds |binary tidyr-1.1.1/tidyr/inst/doc/in-packages.html | 47 +++- tidyr-1.1.1/tidyr/inst/doc/nest.html | 16 + tidyr-1.1.1/tidyr/inst/doc/pivot.html | 118 ++++++----- tidyr-1.1.1/tidyr/inst/doc/programming.html | 18 + tidyr-1.1.1/tidyr/inst/doc/rectangle.html | 131 +++++++------ tidyr-1.1.1/tidyr/inst/doc/tidy-data.html | 16 + tidyr-1.1.1/tidyr/man/complete.Rd | 2 tidyr-1.1.1/tidyr/man/extract.Rd | 2 tidyr-1.1.1/tidyr/man/figures/logo.png |binary tidyr-1.1.1/tidyr/man/gather.Rd | 6 tidyr-1.1.1/tidyr/man/nest_legacy.Rd | 4 tidyr-1.1.1/tidyr/man/reexports.Rd | 2 tidyr-1.1.1/tidyr/man/separate.Rd | 2 tidyr-1.1.1/tidyr/man/spread.Rd | 2 tidyr-1.1.1/tidyr/man/tidyr_legacy.Rd | 2 tidyr-1.1.1/tidyr/man/tidyr_tidy_select.Rd | 2 tidyr-1.1.1/tidyr/man/unite.Rd | 4 tidyr-1.1.1/tidyr/src/cpp11.cpp |only tidyr-1.1.1/tidyr/src/fill.cpp | 11 - tidyr-1.1.1/tidyr/src/melt.cpp | 113 ++++++----- tidyr-1.1.1/tidyr/src/simplifyPieces.cpp | 38 ++- tidyr-1.1.1/tidyr/tests/testthat/test-complete.R | 2 tidyr-1.1.1/tidyr/tests/testthat/test-expand.R | 2 tidyr-1.1.1/tidyr/tests/testthat/test-extract.R | 23 ++ tidyr-1.1.1/tidyr/tests/testthat/test-pack.R | 15 - tidyr-1.1.1/tidyr/tests/testthat/test-separate.R | 17 + 42 files changed, 478 insertions(+), 287 deletions(-)
Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame
like objects, both in memory and out of memory.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>),
Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>),
Lionel Henry [aut],
Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dplyr versions 1.0.0 dated 2020-05-29 and 1.0.1 dated 2020-07-31
DESCRIPTION | 12 - MD5 | 212 +++++++++++++------------- NAMESPACE | 1 NEWS.md | 52 ++++-- R/arrange.R | 24 ++ R/bind.r | 24 ++ R/coalesce.R | 25 ++- R/colwise.R | 2 R/conditions.R | 10 - R/context.R | 13 + R/count-tally.R | 33 +--- R/data-mask.R | 34 +++- R/data-starwars.R | 2 R/doc-params.R | 6 R/filter.R | 3 R/group-by.r | 5 R/group_map.R | 4 R/join-rows.R | 4 R/mutate.R | 28 ++- R/relocate.R | 12 + R/rowwise.r | 2 R/slice.R | 3 R/summarise.R | 42 ++--- R/zzz.r | 5 build/dplyr.pdf |binary build/vignette.rds |binary inst/doc/base.R | 2 inst/doc/base.Rmd | 2 inst/doc/base.html | 134 ++++++++-------- inst/doc/colwise.R | 2 inst/doc/colwise.Rmd | 2 inst/doc/colwise.html | 38 ++-- inst/doc/compatibility.Rmd | 2 inst/doc/compatibility.html | 38 ++-- inst/doc/dplyr.R | 4 inst/doc/dplyr.Rmd | 6 inst/doc/dplyr.html | 42 ++--- inst/doc/grouping.html | 36 ++-- inst/doc/programming.R | 2 inst/doc/programming.Rmd | 4 inst/doc/programming.html | 40 ++-- inst/doc/rowwise.Rmd | 6 inst/doc/rowwise.html | 58 +++---- inst/doc/two-table.Rmd | 2 inst/doc/two-table.html | 44 ++--- inst/doc/window-functions.html | 36 ++-- man/add_rownames.Rd | 2 man/arrange.Rd | 4 man/arrange_all.Rd | 2 man/bind.Rd | 3 man/coalesce.Rd | 3 man/context.Rd | 8 man/count.Rd | 16 - man/distinct_all.Rd | 2 man/dplyr_data_masking.Rd | 2 man/dplyr_tidy_select.Rd | 16 - man/group_by.Rd | 5 man/group_by_all.Rd | 7 man/group_map.Rd | 4 man/mutate.Rd | 2 man/mutate_all.Rd | 2 man/nest_join.Rd | 2 man/pull.Rd | 2 man/reexports.Rd | 8 man/rowwise.Rd | 2 man/scoped.Rd | 2 man/se-deprecated.Rd | 19 -- man/select.Rd | 12 - man/select_all.Rd | 2 man/select_vars.Rd | 2 man/slice.Rd | 2 man/src.Rd | 2 man/src_dbi.Rd | 2 man/starwars.Rd | 2 man/summarise.Rd | 12 + man/summarise_all.Rd | 2 man/tidyeval-compat.Rd | 22 +- src/dplyr.h | 4 src/funs.cpp | 4 src/group_by.cpp | 4 tests/testthat/test-arrange-errors.txt | 2 tests/testthat/test-arrange.r | 14 + tests/testthat/test-bind.R | 11 - tests/testthat/test-coalesce.R | 25 +++ tests/testthat/test-colwise-mutate-errors.txt | 6 tests/testthat/test-colwise-mutate.R | 12 + tests/testthat/test-context-error.txt | 3 tests/testthat/test-context.R | 15 + tests/testthat/test-count-tally.r | 20 -- tests/testthat/test-count-tally.txt | 10 - tests/testthat/test-filter-errors.txt | 14 - tests/testthat/test-filter.r | 14 + tests/testthat/test-group-by.r | 6 tests/testthat/test-join.r | 13 + tests/testthat/test-mutate-errors.txt | 27 ++- tests/testthat/test-mutate.r | 46 +++++ tests/testthat/test-relocate.R | 17 ++ tests/testthat/test-summarise-errors.txt | 19 +- tests/testthat/test-summarise.r | 17 ++ tests/testthat/test-window.R | 8 vignettes/base.Rmd | 2 vignettes/colwise.Rmd | 2 vignettes/compatibility.Rmd | 2 vignettes/dplyr.Rmd | 6 vignettes/programming.Rmd | 4 vignettes/rowwise.Rmd | 6 vignettes/two-table.Rmd | 2 107 files changed, 970 insertions(+), 596 deletions(-)
Title: A Permutation Based Test for Biomarker Discovery in Microbiome
Data
Description: The permubiome R package was created to perform a permutation-based non-parametric analysis on microbiome data for biomarker discovery aims. This test executes thousands of comparisons in a pairwise manner, after a random shuffling of data into the different groups of study with a prior selection of the microbiome features with the largest variation among groups. Previous to the permutation test itself, data can be normalized according to different methods proposed to handle microbiome data ('proportions' or 'Anders'). The median-based differences between groups resulting from the multiple simulations are fitted to a normal distribution with the aim to calculate their significance. A multiple testing correction based on Benjamini-Hochberg method (fdr) is finally applied to extract the differentially presented features between groups of your dataset. LATEST UPDATES: v1.1 and olders incorporates function to parse COLUMN format; v1.2 and olders incorporates -optimize- function to maximize evaluation of features with largest inter-class variation; v1.3 and olders includes the -size.effect- function to perform estimation statistics using the bootstrap-coupled approach implemented in the 'dabestr' (>=0.3.0) R package.
Author: Alfonso Benitez-Paez
Maintainer: Alfonso Benitez-Paez <alfbenpa@gmail.com>
Diff between permubiome versions 1.3 dated 2019-12-10 and 1.3.1 dated 2020-07-31
DESCRIPTION | 14 +++++++------- MD5 | 20 ++++++++++---------- NAMESPACE | 3 ++- R/plots.R | 2 +- R/size.effect.R | 29 ++++++++++++++++------------- man/get.data.Rd | 3 ++- man/normalize.Rd | 3 ++- man/optimize.Rd | 3 ++- man/permutation.Rd | 3 ++- man/plots.Rd | 5 +++-- man/size.effect.Rd | 52 +++++++++++++++++++++++++++++----------------------- 11 files changed, 76 insertions(+), 61 deletions(-)
Title: Maximum Likelihood Estimation and Related Tools
Description: Functions for Maximum Likelihood (ML) estimation, non-linear
optimization, and related tools. It includes a unified way to call
different optimizers, and classes and methods to handle the results from
the Maximum Likelihood viewpoint. It also includes a number of convenience tools for testing
and developing your own models.
Author: Ott Toomet <otoomet@gmail.com>,
Arne Henningsen <arne.henningsen@gmail.com>,
with contributions from Spencer Graves and Yves Croissant
Maintainer: Ott Toomet <otoomet@gmail.com>
Diff between maxLik versions 1.3-8 dated 2020-01-10 and 1.4-0 dated 2020-07-31
DESCRIPTION | 19 ++--- MD5 | 79 ++++++++++++-------- NAMESPACE | 6 + NEWS | 21 +++++ R/10-MaxControl_class.R | 114 +++++++++++++++++++++++++++--- R/25-addControlList.R | 22 +++++ R/30-addControlDddot.R | 2 R/checkFuncArgs.R | 3 R/compareDerivatives.R | 35 +++++---- R/gradient.R | 2 R/head....R |only R/logLikAttr.R | 10 +- R/logLikFunc.R | 16 ++-- R/logLikGrad.R | 3 R/logLikHess.R | 2 R/maxAdam.R |only R/maxNRCompute.R | 3 R/maxSGA.R |only R/maxSGACompute.R |only R/maximMessage.R | 5 - R/openParam.R | 2 R/printRowColLimits.R |only R/storedParameters.R |only R/storedValues.R |only R/sumGradients.R | 3 R/summary.maxim.R | 9 +- R/zzz.R | 13 +++ build |only inst/doc |only man/compareDerivatives.Rd | 11 ++ man/maxBFGS.Rd | 2 man/maxControl.Rd | 71 ++++++++++++++++-- man/maxLik-internal.Rd | 1 man/maxLik-package.Rd | 36 +++++++-- man/maxNR.Rd | 8 -- man/maxSGA.Rd |only man/returnCode.Rd | 30 +++++++ man/storedValues.Rd |only man/summary.maxim.Rd | 15 +++ tests/fitNormalDist_privateTest.Rout.save | 42 ----------- tests/maxControl_privateTest.Rout.save |only tests/maxSG_privateTest.Rout.save |only tests/methods.R | 23 ++++++ tests/methods.Rout.save | 89 ++++++++++++++++++++++- tests/parameters_privateTest.Rout.save | 47 +++++++++++- vignettes |only 46 files changed, 573 insertions(+), 171 deletions(-)
Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory
factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre] (<https://orcid.org/0000-0002-4129-4477>),
Terrence D. Jorgensen [aut] (<https://orcid.org/0000-0001-5111-6773>),
Nicholas Rockwood [aut] (<https://orcid.org/0000-0001-5931-183X>),
Daniel Oberski [ctb],
Jarrett Byrnes [ctb],
Leonard Vanbrabant [ctb],
Victoria Savalei [ctb],
Ed Merkle [ctb],
Michael Hallquist [ctb],
Mijke Rhemtulla [ctb],
Myrsini Katsikatsou [ctb],
Mariska Barendse [ctb],
Florian Scharf [ctb]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>
Diff between lavaan versions 0.6-6 dated 2020-05-13 and 0.6-7 dated 2020-07-31
lavaan-0.6-6/lavaan/R/lav_fiml.R |only lavaan-0.6-7/lavaan/DESCRIPTION | 11 lavaan-0.6-7/lavaan/MD5 | 77 ++--- lavaan-0.6-7/lavaan/R/lav_bootstrap.R | 21 + lavaan-0.6-7/lavaan/R/lav_bootstrap_lrt.R | 1 lavaan-0.6-7/lavaan/R/lav_bvmix.R | 52 +++ lavaan-0.6-7/lavaan/R/lav_bvord.R | 42 ++- lavaan-0.6-7/lavaan/R/lav_bvreg.R | 67 ++++ lavaan-0.6-7/lavaan/R/lav_data.R | 45 ++- lavaan-0.6-7/lavaan/R/lav_efa_extraction.R | 305 +++++++++++++++++++++- lavaan-0.6-7/lavaan/R/lav_matrix.R | 21 + lavaan-0.6-7/lavaan/R/lav_model_efa.R | 121 ++++++++ lavaan-0.6-7/lavaan/R/lav_model_estimate.R | 43 +++ lavaan-0.6-7/lavaan/R/lav_model_information.R | 5 lavaan-0.6-7/lavaan/R/lav_model_loglik.R | 10 lavaan-0.6-7/lavaan/R/lav_model_objective.R | 2 lavaan-0.6-7/lavaan/R/lav_mvnorm.R | 27 - lavaan-0.6-7/lavaan/R/lav_mvnorm_h1.R | 17 - lavaan-0.6-7/lavaan/R/lav_mvnorm_missing_h1.R | 15 - lavaan-0.6-7/lavaan/R/lav_mvreg.R | 8 lavaan-0.6-7/lavaan/R/lav_object_inspect.R | 3 lavaan-0.6-7/lavaan/R/lav_object_methods.R | 8 lavaan-0.6-7/lavaan/R/lav_objective.R | 6 lavaan-0.6-7/lavaan/R/lav_options.R | 22 + lavaan-0.6-7/lavaan/R/lav_partable.R | 87 +++++- lavaan-0.6-7/lavaan/R/lav_partable_flat.R | 21 + lavaan-0.6-7/lavaan/R/lav_partable_unrestricted.R | 2 lavaan-0.6-7/lavaan/R/lav_partable_vnames.R | 47 ++- lavaan-0.6-7/lavaan/R/lav_predict.R | 108 ++++--- lavaan-0.6-7/lavaan/R/lav_representation_lisrel.R | 16 + lavaan-0.6-7/lavaan/R/lav_samplestats.R | 21 + lavaan-0.6-7/lavaan/R/lav_standardize.R | 2 lavaan-0.6-7/lavaan/R/lav_start.R | 40 ++ lavaan-0.6-7/lavaan/R/lav_syntax.R | 25 + lavaan-0.6-7/lavaan/R/xxx_fsr.R | 12 lavaan-0.6-7/lavaan/R/xxx_lavaan.R | 188 ++++++++++++- lavaan-0.6-7/lavaan/man/lavOptions.Rd | 4 lavaan-0.6-7/lavaan/man/lavPredict.Rd | 6 lavaan-0.6-7/lavaan/man/lav_matrix.Rd | 5 lavaan-0.6-7/lavaan/man/model.syntax.Rd | 23 + 40 files changed, 1287 insertions(+), 249 deletions(-)
Title: Melting Temperature of Nucleic Acid Sequences
Description: This tool is extended from methods in Bio.SeqUtils.MeltingTemp of python. The melting temperature of nucleic acid sequences can be calculated in three method, the Wallace rule (Thein & Wallace (1986) <doi:10.1016/S0140-6736(86)90739-7>), empirical formulas based on G and C content (Marmur J. (1962) <doi:10.1016/S0022-2836(62)80066-7>, Schildkraut C. (2010) <doi:10.1002/bip.360030207>, Wetmur J G (1991) <doi:10.3109/10409239109114069>, Untergasser,A. (2012) <doi:10.1093/nar/gks596>, von Ahsen N (2001) <doi:10.1093/clinchem/47.11.1956>) and nearest neighbor thermodynamics (Breslauer K J (1986) <doi:10.1073/pnas.83.11.3746>, Sugimoto N (1996) <doi:10.1093/nar/24.22.4501>, Allawi H (1998) <doi:10.1093/nar/26.11.2694>, SantaLucia J (2004) <doi:10.1146/annurev.biophys.32.110601.141800>, Freier S (1986) <doi:10.1073/pnas.83.24.9373>, Xia T (1998) <doi:10.1021/bi9809425>, Chen JL (2012) <doi:10.1021/bi3002709>, Bommarito S (2000) <doi:10.1093/nar/28.9.1929>, Turner D H (2010) <doi:10.1093/nar/gkp892>, Sugimoto N (1995) <doi:10.1016/S0048-9697(98)00088-6>, Allawi H T (1997) <doi:10.1021/bi962590c>, Santalucia N (2005) <doi:10.1093/nar/gki918>), and it can also be corrected with salt ions and chemical compound (SantaLucia J (1996) <doi:10.1021/bi951907q>, SantaLucia J(1998) <doi:10.1073/pnas.95.4.1460>, Owczarzy R (2004) <doi:10.1021/bi034621r>, Owczarzy R (2008) <doi:10.1021/bi702363u>).
Author: Junhui Li
Maintainer: Junhui Li <junhuili@cau.edu.cn>
Diff between TmCalculator versions 1.0.0 dated 2019-02-11 and 1.0.1 dated 2020-07-31
TmCalculator-1.0.0/TmCalculator/R/TmCalculator-internal.R |only TmCalculator-1.0.1/TmCalculator/DESCRIPTION | 10 +++++----- TmCalculator-1.0.1/TmCalculator/MD5 | 7 +++---- TmCalculator-1.0.1/TmCalculator/R/salt_correction.R | 11 +++++++---- TmCalculator-1.0.1/TmCalculator/man/TmCalculator-package.Rd | 4 ++-- 5 files changed, 17 insertions(+), 15 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
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